OK, now I understand what's the problem. You can do this in Vertabelo.

Let's say you start from this point:





First, just create a reference from B to A:





Here, we get an autogenerated "B_contact_code" column. Just delete it:





An error is raised because there's no FK column defined in the reference. We just need to fix it. Select a reference and here's what we see:





Just click "X" on the right-hand side to delete this invalid pair of columns:





and then add a valid ones:






Done, we've got what we wanted:






We can also eliminate the need to delete this autogenerated column. It is possible to disable the generation of FK columns. You can do this on "My account" page:





Hope this helps!

Vertabelo already supports generating Extended Properties. You just need to select "Generate comments for database objects" checkbox: